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Wang J, Zhang Y, Gao J, Feng G, Liu C, Li X, Li P, Liu Z, Lu F, Wang L, Li W, Zhou Q, Liu Y. Alternative splicing of CARM1 regulated by LincGET-guided paraspeckles biases the first cell fate in mammalian early embryos. Nat Struct Mol Biol 2024:10.1038/s41594-024-01292-9. [PMID: 38658621 DOI: 10.1038/s41594-024-01292-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
The heterogeneity of CARM1 controls first cell fate bias during early mouse development. However, how this heterogeneity is established is unknown. Here, we show that Carm1 mRNA is of a variety of specific exon-skipping splicing (ESS) isoforms in mouse two-cell to four-cell embryos that contribute to CARM1 heterogeneity. Disruption of paraspeckles promotes the ESS of Carm1 precursor mRNAs (pre-mRNAs). LincGET, but not Neat1, is required for paraspeckle assembly and inhibits the ESS of Carm1 pre-mRNAs in mouse two-cell to four-cell embryos. We further find that LincGET recruits paraspeckles to the Carm1 gene locus through HNRNPU. Interestingly, PCBP1 binds the Carm1 pre-mRNAs and promotes its ESS in the absence of LincGET. Finally, we find that the ESS seen in mouse two-cell to four-cell embryos decreases CARM1 protein levels and leads to trophectoderm fate bias. Our findings demonstrate that alternative splicing of CARM1 has an important role in first cell fate determination.
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Affiliation(s)
- Jiaqiang Wang
- College of Life Science, Northeast Agricultural University, Harbin, China.
| | - Yiwei Zhang
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Jiaze Gao
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xueke Li
- College of Life Science, Northeast Agricultural University, Harbin, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Pengcheng Li
- College of Life Science, Northeast Agricultural University, Harbin, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhonghua Liu
- College of Life Science, Northeast Agricultural University, Harbin, China
| | - Falong Lu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Leyun Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
| | - Yusheng Liu
- College of Life Science, Northeast Forestry University, Harbin, China.
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2
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Kang SWS, Cunningham RP, Miller CB, Brown LA, Cultraro CM, Harned A, Narayan K, Hernandez J, Jenkins LM, Lobanov A, Cam M, Porat-Shliom N. A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling. Nat Commun 2024; 15:1799. [PMID: 38418824 PMCID: PMC10902380 DOI: 10.1038/s41467-024-45751-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 02/04/2024] [Indexed: 03/02/2024] Open
Abstract
In the liver, mitochondria are exposed to different concentrations of nutrients due to their spatial positioning across the periportal and pericentral axis. How the mitochondria sense and integrate these signals to respond and maintain homeostasis is not known. Here, we combine intravital microscopy, spatial proteomics, and functional assessment to investigate mitochondrial heterogeneity in the context of liver zonation. We find that periportal and pericentral mitochondria are morphologically and functionally distinct; beta-oxidation is elevated in periportal regions, while lipid synthesis is predominant in the pericentral mitochondria. In addition, comparative phosphoproteomics reveals spatially distinct patterns of mitochondrial composition and potential regulation via phosphorylation. Acute pharmacological modulation of nutrient sensing through AMPK and mTOR shifts mitochondrial phenotypes in the periportal and pericentral regions, linking nutrient gradients across the lobule and mitochondrial heterogeneity. This study highlights the role of protein phosphorylation in mitochondrial structure, function, and overall homeostasis in hepatic metabolic zonation. These findings have important implications for liver physiology and disease.
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Affiliation(s)
- Sun Woo Sophie Kang
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rory P Cunningham
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Colin B Miller
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Lauryn A Brown
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Constance M Cultraro
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Adam Harned
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Research Technology Programs, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kedar Narayan
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Research Technology Programs, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jonathan Hernandez
- Surgical Oncology Program, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Alexei Lobanov
- CCR Collaborative Bioinformatics Resource (CCBR) National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource (CCBR) National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Natalie Porat-Shliom
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA.
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3
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Porat-Shliom N. Compartmentalization, cooperation, and communication: The 3Cs of Hepatocyte zonation. Curr Opin Cell Biol 2024; 86:102292. [PMID: 38064779 PMCID: PMC10922296 DOI: 10.1016/j.ceb.2023.102292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 02/15/2024]
Abstract
The unique architecture of the liver allows for spatial compartmentalization of its functions, also known as liver zonation. In contrast to organelles and cells, this compartment is devoid of a surrounding membrane, rendering traditional biochemical tools ineffective for studying liver zonation. Recent advancements in tissue imaging and single-cell technologies have provided new insights into the complexity of tissue organization, rich cellular composition, and the gradients that shape zonation. Hepatocyte gene expression profiles and metabolic programs differ based on their location. Non-parenchymal cells further support hepatocytes from different zones through local secretion of factors that instruct hepatocyte activities. Collectively, these elements form a cohesive and dynamic network of cell-cell interactions that vary across space, time, and disease states. This review will examine the cell biology of hepatocytes in vivo, presenting the latest discoveries and emerging principles that govern tissue-level and sub-cellular compartmentalization.
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Affiliation(s)
- Natalie Porat-Shliom
- Cell Biology and Imaging Section, Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
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4
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Cunningham RP, Kang SWS, Porat-Shliom N. Location matters: cellular heterogeneity in the hepatic lobule and hepatocellular carcinoma. Am J Physiol Gastrointest Liver Physiol 2023; 324:G245-G249. [PMID: 36749570 PMCID: PMC10010932 DOI: 10.1152/ajpgi.00278.2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Tumor heterogeneity is a hallmark of cancer but a challenging problem to dissect mechanistically. Less recognized is that cells within normal tissues are also remarkably diverse. Hepatocytes are a great example because their spatial positioning and the local microenvironment govern their genetic heterogeneity. Recent studies show that primary liver tumors display heterogeneity similar to that observed in the normal tissue providing clues to the cellular precursor of the tumor and how variations in the lobule microenvironment support tumor formation and aggressiveness. Identifying the principles that control cellular diversity in a healthy liver may highlight potential mechanisms driving hepatic tumor heterogeneity.
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Affiliation(s)
- Rory P Cunningham
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Sun Woo Sophie Kang
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Natalie Porat-Shliom
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
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